Changes between Version 77 and Version 78 of SOPs/mapping


Ignore:
Timestamp:
05/24/22 15:15:48 (3 years ago)
Author:
byuan
Comment:

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  • SOPs/mapping

    v77 v78  
    102102  * '''--phred33-quals'''         (default "Sanger format"; for input quality scores from Illumina versions 1.8 and later)
    103103
     104As mentioned in the [http://bowtie-bio.sourceforge.net/manual.shtml bowtie manual] : "Paired-end alignments where one mate’s alignment is entirely contained within the other’s are considered invalid." In this case, you can trim one base off from 3 prime end of each read, as suggested by [https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md#paired-end-specific-options trim_galore documentation]
     105
    104106To see other parameters log into tak and type '''bowtie'''
    105107